It doesn't. That is like saying that if someone structures their affairs to pay less taxes it implies that wanted to do something illegal. They had to choose some structure, they picked the safest and easiest one. In both the hypothetical tax case and the real MS case, I suspect.
The incentive is to choose structures that minimise regulatory engagement. The fact that MS is following incentives isn't a red flag. Not a green one either, it isn't interesting except as something that the NYTimes can hook insinuations on.